Coexpression cluster:C1034

Full id: C1034_pituitary_olfactory_amygdala_insula_temporal_hippocampus_frontal

Phase1 CAGE Peaks

Hg19::chr14:62584201..62584208,+	p1@ENST00000334389
Hg19::chr16:1383632..1383652,+	p1@BAIAP3
Hg19::chr1:204320105..204320146,-	p@chr1:204320105..204320146 -
Hg19::chr2:220379118..220379131,+	p1@ACCN4
Hg19::chr6:69942915..69942931,+	p@chr6:69942915..69942931 +
Hg19::chr6:69942947..69942963,+	p@chr6:69942947..69942963 +
Hg19::chr6:69942992..69943002,+	p@chr6:69942992..69943002 +
Hg19::chrX:101397536..101397555,+	p@chrX:101397536..101397555 +

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0015081	sodium ion transmembrane transporter activity	0.0170718784065629
GO:0007269	neurotransmitter secretion	0.0380050197822336
GO:0045055	regulated secretory pathway	0.0380050197822336
GO:0005272	sodium channel activity	0.0380050197822336
GO:0003001	generation of a signal involved in cell-cell signaling	0.0380050197822336
GO:0008022	protein C-terminus binding	0.0380050197822336
GO:0001505	regulation of neurotransmitter levels	0.0380050197822336
GO:0031402	sodium ion binding	0.0409176272807585

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	1.57e-93	56
neural rod	1.57e-93	56
future spinal cord	1.57e-93	56
neural keel	1.57e-93	56
nervous system	6.21e-92	89
central nervous system	2.72e-89	81
regional part of nervous system	3.02e-86	53
regional part of brain	3.02e-86	53
regional part of forebrain	2.27e-79	41
forebrain	2.27e-79	41
anterior neural tube	2.27e-79	41
future forebrain	2.27e-79	41
brain	6.65e-78	68
future brain	6.65e-78	68
telencephalon	1.89e-70	34
brain grey matter	2.42e-70	34
gray matter	2.42e-70	34
neural plate	7.25e-69	82
presumptive neural plate	7.25e-69	82
cerebral hemisphere	5.16e-66	32
regional part of telencephalon	1.61e-65	32
neurectoderm	4.39e-65	86
pre-chordal neural plate	1.97e-59	61
ecto-epithelium	2.66e-56	104
regional part of cerebral cortex	2.98e-56	22
adult organism	1.70e-52	114
neocortex	2.69e-51	20
cerebral cortex	5.46e-49	25
pallium	5.46e-49	25
ectoderm-derived structure	1.03e-46	171
ectoderm	1.03e-46	171
presumptive ectoderm	1.03e-46	171
structure with developmental contribution from neural crest	9.99e-42	132
organ system subdivision	6.29e-38	223
basal ganglion	7.86e-23	9
nuclear complex of neuraxis	7.86e-23	9
aggregate regional part of brain	7.86e-23	9
collection of basal ganglia	7.86e-23	9
cerebral subcortex	7.86e-23	9
neural nucleus	1.73e-22	9
nucleus of brain	1.73e-22	9
tube	8.33e-20	192
telencephalic nucleus	7.79e-18	7
anatomical cluster	2.02e-17	373
gyrus	2.31e-17	6
posterior neural tube	1.00e-15	15
chordal neural plate	1.00e-15	15
occipital lobe	3.90e-15	5
temporal lobe	9.90e-15	6
parietal lobe	1.20e-14	5
limbic system	4.98e-14	5
organ part	1.32e-13	218
anatomical conduit	1.87e-13	240
segmental subdivision of nervous system	1.09e-11	13
corpus striatum	1.96e-11	4
striatum	1.96e-11	4
ventral part of telencephalon	1.96e-11	4
future corpus striatum	1.96e-11	4
epithelium	2.85e-11	306
cell layer	4.86e-11	309
brainstem	6.15e-11	6
diencephalon	2.29e-10	7
future diencephalon	2.29e-10	7
segmental subdivision of hindbrain	7.09e-10	12
hindbrain	7.09e-10	12
presumptive hindbrain	7.09e-10	12
multi-tissue structure	2.62e-09	342
frontal cortex	2.64e-09	3
germ layer	4.05e-09	560
germ layer / neural crest	4.05e-09	560
embryonic tissue	4.05e-09	560
presumptive structure	4.05e-09	560
germ layer / neural crest derived structure	4.05e-09	560
epiblast (generic)	4.05e-09	560
caudate-putamen	6.01e-09	3
dorsal striatum	6.01e-09	3
embryonic structure	6.14e-09	564
spinal cord	1.14e-08	3
dorsal region element	1.14e-08	3
dorsum	1.14e-08	3
pons	1.27e-08	3
embryo	2.43e-08	592
organ	3.14e-08	503
developing anatomical structure	3.37e-08	581
pituitary gland	2.72e-07	2
regional part of metencephalon	3.88e-07	9
metencephalon	3.88e-07	9
future metencephalon	3.88e-07	9
anatomical system	4.59e-07	624
anatomical group	5.01e-07	625
middle temporal gyrus	5.95e-07	2
middle frontal gyrus	9.10e-07	2

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
E2F6#1876	5	3.13572233231087	0.0102488050142096	0.0381500141454552
GATA2#2624	4	6.372465866777	0.00204874075705145	0.0118950653727872
GATA3#2625	3	10.2136936339523	0.00241087012618913	0.0135896408197898
HDAC2#3066	5	8.38476264789141	0.00010628730938187	0.00148086183358233
MAX#4149	6	4.83941663175534	0.000291750431370536	0.00309750160637465
MXI1#4601	4	4.98078581437965	0.00509441532042917	0.0236964165879972
RAD21#5885	4	5.17751694772816	0.00442059452597695	0.0209408296683679
REST#5978	4	4.82501435806401	0.00572073539826954	0.0257851574925499
SIN3A#25942	5	3.38055295425946	0.00734222696117028	0.0303628921638354
SUZ12#23512	4	25.0578904555315	1.03898994633546e-05	0.000270129626600273
ZNF263#10127	4	4.11092081850534	0.0101999278231626	0.0379910935065365

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.